It's Volcano Day, Captain
by vertigoSWAY
Summary: The Doctor goes undercover as William Clark with Amy as they land on the first New Earth where a certain Captain is trying to wipe out a mutant group. But when the Doctor starts getting edgy, can Amy figure out what links the Doctor to the Captain?
1. Deja Vu

**To avoid any continuity errors as I wrote this after Time of Angels aired, but before Flesh and Stone, this story is AU from Flesh and Stone. Or something. **

**

* * *

**

"Have you ever learned how to drive a car?" Amy asked as she held on to the rails for her dear life.

"Yes. Why?" the Doctor called from the other side of the TARDIS console. He was busy turning knobs and flipping switches.

"Because you don't use the stabilizers on purpose. It gets a bit bumpy in here."

"It's a mauve alert. Intergalactic equivalent for red alert. That's where you humans get red from. Long long time ago, back when UNIT was formed. Sometimes Earth can be so unoriginal, but camping. You lot are the only ones who do that!"

"Alert? What's wrong?"

"Don't know," the Doctor marveled. "Let's find out shall we?"

* * *

"So where are we now?" Amy stepped out and saw nothing but dingy high-rises and muck filled streets with hover cars.

"New Earth," the Time Lord remarked, coming out of the TARDIS. He snapped his fingers and the door closed.

"How do you lock it?" Amy asked.

"Lock what? The TARDIS? She's clever enough to not let her get stolen. She's alive you know."

"She's a _she_?"

"Well humans called their ships 'shes' don't they?"

"But you had a key before."

"Way back when. Don't need it anymore. Here ya go." The eleventh Doctor tossed the golden key to Amy. "More use of it for you now. Don't lose it."

"Why me?"

"Why not you Amy Pond? Amelia, Amelia, Amy Pond."

"Alright, stop that. It's getting a bit irritating."

"Am I irritating?"

"Sometimes, maybe."

"Not rude though?"

Amy shrugged. "We're in the future? Looks like Starship UK."

"It's way earlier than that. I'd say only one thousand years from 2010, but based on the smell of the air… we're on the other side of the galaxy from where Starship UK stood."

"You can tell that from the smell of the air?"

"Pollution levels. Not hard. Oi wait. What's that?" The Doctor pointed off into the distance.

"Looks like a fight."

"Well then. Come on!"

"Wait!" Amy shouted after him as they ran towards the scene. She stopped against the Time Lord's outstretched hand. She followed his gaze to the scene. There were at least five bandits, undoubtedly human besides the fact that they were genetically altered to have abnormal body parts. In the center was one man trying to fend them off. Amy watched in horror as the man injured and killed all five.

"He wouldn't do that," the Doctor whispered. He was unaware that Amy heard him. "Let's go. Now." He turned around with the intention of running back to the TARDIS behind the hill but shouted as a self-programmed military weapon flew straight towards him. He ducked along with Amy as the other man shot down the weapon.

"Hey!" the man cried. "What the hell do you think you're doing?"

The Doctor got up and smiled feebly, knowing there was no way out of this situation. "Hello! Sorry for the trouble."

"You don't want to be out here during this time of day when there's war going on." The man approached them and Amy could feel the Doctor stiffen. Was he afraid? Surely the mighty Time Lord couldn't be scared of one man.

"Yeah. Like I said before sorry."

"Who are you? Never seen the two of you around."

"I'm…" the Doctor searched for a suitable name. "William Clark," he finally came up with. "This is Amy Pond. We grew up together."

"Childhood friends?"

"Something of the sort."

"Nice to meet you," the man nodded. "Captain Jack Harkness."

"Captain? Of what?" Amy asked.

"Amy, that's rude to ask. He probably doesn't want to tell you," the Doctor whispered.

"The title used to mean something. Now it doesn't. Come on. Let me get you to the Silo."

"Silo?" the Doctor remarked at the familiarity of the name.

* * *

Amy marveled at the complexity of the underground haven. There was still electricity and running water, as well as food and other scavenged necessities. She didn't understand why the Doctor was afraid of this man. He was nice enough to them, even giving them a bedroom. The Doctor had to ruin the moment by pulling out his knowledge.

"What's that?" the Time Lord asked, nodding to the box on the wall.

"Transducer," Harkness replied. "Sometimes the Silo doesn't get enough electricity. We have to fine our own ways to power up this place up."

The Doctor peered at it closely. The covering was transparent, revealing circuit boards and wires beneath the control buttons. "Looks wired enough to set up an explosion. Look at that, parallel circuits wherever you can fit them. Guaranteed energy. And Silo? Where did you come up with that name? Wasn't that something used for storing grain in the ancient times?" Harkness raised his eyebrows while Amy visibly rolled her eyes. "I'm a scholar," the Doctor supplied.

The captain nodded in understanding. "Then you wouldn't mind helping my team?"

"You've got a team?"

The man led them up to the end of a hallway. There was nothing but a big brick wall. "There's nothing there," Amy pointed out.

_The corner of your eye_, the Doctor thought.

Harkness laughed. "That's where you're wrong." He pushed up his sleeve and pressed a few buttons on his wrist strap. "Welcome to 31st Century Torchwood."

The brick had rippled away to reveal the most amazing secret headquarters Amy Pond had ever seen in her life. It was just like the films. All polished silvery and glittering. "The stars are like diamonds," the Doctor muttered.

"What was that?" Amy asked.

"Nothing," the Time Lord dismissed quickly. "So Torchwood," the Doctor exclaimed loudly. "What's that?" While he was speaking, three people –one man and two women- came out. All were very young.

"William Clark and Amy Pond, meet Rhea, Miriam and David. Torchwood. We fight aliens."

"That's interesting. You a secret to the world? Never heard of you."

"We try to be undercover," Harkness replied.

"Worked for me." The Doctor flashed a smile.

"What's he doing here?" the man named David asked.

"More importantly who is he?" Rhea put in.

"Everyone, meet William Clark and Amy Pond," the captain introduced. "Apparently William here's a bit of a genius."

"He's just exaggerating," interrupted the Time Lord.

"He's here to help."

"With what?" Rhea inquired.

"Yeah Captain," the Doctor agreed. "Still don't know what I'm signing up for."

"And why are their clothes clean?" Miriam finally asked.

Everyone turned to stare at them, noticing the obvious for the first time. Usually the survivors that were found had shabby clothes. A rip in the pants here, a scorch in a shirt there. And they most definitely did not dress in layers. On top of that, they had bruises, cuts and scrapes all over them. These two, however, did not.

"Uh, well," the Doctor began. "Always quick on our feet. This isn't the first time we've been in a crisis before. You learn to survive after a while don't you?" The Doctor must have given an honest answer because the Torchwood team accepted it easily. Amy cast her Time Lord friend a quizzical glance. The Doctor just looked back and looked away quickly.

"Come on," Harkness said. "I'll show you what you'll be helping us with."


	2. Poker Face

The leader or Torchwood led the two time travelers down the corridor faintly reminiscent of the Silo at the end of the universe. The Doctor followed along stubbornly with that slight frustrated look on his face. This prompted Amy to tease him. "Oh Mr. Grumpy Face again?" she laughed quietly. The Doctor shot her a glare. Amy was taken aback. "You know him?" she asked softly. The hum of the machines drowned out her voice from Harkness

The Doctor looked at Amy and replied enigmatically, "Not this man."

Amy was puzzled and was about to question again when they reached the end of the hall. To the left was a sectioned off control room. There was a beat computer, switches and buttons all over the walls. "Ooh busy bee," the Doctor remarked. He feigned his wondrousness quite nicely. "Very, very busy." He stepped in a swept around, surveying the room with his hands halfway in the air and at his side. "What's all this for?" he pointed and looked at the captain. "No wait hold on." He surveyed the room again. "Controls are for-"

"It's linked up to the transducer," explained the captain.

"You want more light?" the Doctor exclaimed bewilderedly.

"There's an alien invasion. Where've you been?"

"Really?" the Time Lord responded. His face was scrunched up. "Amy!" Why don't you tell me? Blimey, that thump on the head must've been hard."

"Well I'm sorry," Amy played along. "You were too busy _talking_."

"We received a transmission from the mother ship," Harkness said.

"And now you want to blow it out of the sky?" finished the Doctor.

"They're a threat."

"Diplomacy? Negotiation?"

"We're at war! We didn't start it. They attacked us first."

"Yes wait but hold on, the mutants on that street. Who were they?"

"Those aren't mutants William. They're a whole different species." The Doctor looked at the captain quizzically. "They attacked us. Someone tipped us off that more were coming and then the message came in. It's getting late. I'll get Rhea to show you where you can stay."

* * *

Rhea was a tall skinny woman with brown hair down to her shoulders. It was parted from the right to the left and graced her left shoulder with a smooth ponytail. Amy reckoned that she'd be an actress or a model if she were back in 21st century London. "Where is this place anyway?" Amy piped up. "'Cause I mean, Will and I've been running for how long? We kind of lost track of direction." She added a wink in the Time Lord's direction that told him he had some explaining to do.

"It's New Cardiff."

"Because they've got an old one too," Amy laughed.

"No," Rhea started. "Because it's New Earth. You're Scottish."

"Yeah," the Doctor cut in. "Up from New Glasgow. I moved up there a long long time ago. How we met each other."

"Well I don't blame either of you for not having straight bearings. Information gets broken and changed over long distances in times like these."

"Oh and the captain of yours," Amy went on. "Quite a looker isn't he? Though he's a bit old for me."

"Amy," the Time Lord said with complaint.

"Good luck trying to get anything out of him," Rhea laughed. "He's not much of a romancer."

"Now really?" The Doctor was surprised. "Why's that?" In the back of his mind, he assumed he already knew the answer.

"Don't really know. He doesn't talk to us much if it's not Torchwood related. We don't know anything about him actually."

"But you trust him?" Amy questioned. "I mean, he could be leading the aliens straight for us and you'd never know."

"Who else can we trust?" Rhea asked. "Besides, I don't think he's like that. By that look in his eyes, it's like he's lost something and he's trying to keep from forgetting." They stopped in front of a metal door. "Here you are then. There's a lock on the inside for privacy. Sweet dreams hopefully."

When the Doctor and Amy were left in their little room with two makeshift beds, Amy said, "Explain. Again. First River and now this."

"I don't know what you're talking about," denied the Time Lord, sitting down on his bed.

"Aw Mr. Grumpy Face."

"Amelia!" snapped the Doctor. Amy jumped back. "Sorry. Do you have a headache?"

"What?"

"You have a headache don't you?"

"What are you talking about?"

"The air outside always gives you headaches. Come here."

"A-alright." Amy said down next to the Doctor. He started to rub her temples.

_Don't panic. Think yes if you can hear me._ Amy was a bit startled to here the Doctor's voice in her head.

_Yes._

The Doctor let go. "Alright! Feel better now?" _It's a telepathic link. There's a camera in the top right corner, don't look now. The room has been bugged._ "Headache should be gone by morning," _No, don't listen to my voice. Listen to me inside your head. Follow my lead all the time. _"You'll feel better later. How are you now?" _And don't try to talk while you're thinking to me like I am. You don't have the coordination. If you understand say out loud "It's a bit better."_

"It's a bit better," obeyed Amy.

"Well that's good." The Doctor clapped his hands together. "Now get to sleep. Big day tomorrow." There was a small candle on the ground in between them along with what looked like a lighter. The Doctor blew out the candle after Amy returned to her bed and lay down on it. She faced away from the Doctor. Each had their backs to each other.

_It's a two way link. _The Doctor's voice found her mind again. _What was it that you wanted to tell me?_

_Do you know him?_

There was no reply for a while and Amy was afraid that the Doctor had fallen asleep. That would have been a record. _No_, the Doctor replied finally. _I told you. Not this man._

_But what does that _mean_? _ Amy pleaded.

_It means what it means._

_Is it like River Song? You're going to keep meeting him one way or another except he's your past and you're his future? This is going to be the first time he ever sees you. And that's why you can't let the cameras or bugs here._

_Not quite. He knows me… from a long long long time ago. But my face has changed. I'm not the Time Lord he knew anymore and it's better that way._

_ You're just going to run away again? You're the one yabbering about timelines and all that._

_ I also yabber about not interfering with events in time._

_ And yet you do anyway._

_ I'm afraid Amy, is that alright? I'm scared and that's the truth. I'm scared of what he's going to do when he finds out and I'm scared to face him because of what I did in his past –or rather what I didn't do. But we also have to fix this._

_ So you want to run away but you can't. Is your life always this complicated?_

_ Yes._

_ How do you keep up? How I'm supposed to keep up?_

_ You don't. But Amy, you have to promise me one thing._

_ What?_

_ I'm not the Doctor here. My name is William Clark who happens to be terribly magnificent, do you understand me? And you're just Amy Pond, just a normal Scottish girl. You don't know much about aliens. Not a word about the Atraxi, Prisoner Zero, the Daleks, Starship UK or the Angels or anything. No TARDIS, no Time Lords._

_ Hang on. What about the TARDIS? We can't just leave it parked out there._

_ She's smart enough the take care of herself. You can't see her unless you try, perception filter. But Amy, do you understa-_

_ Yeah I know. No such thing as the Doctor. Just some bloke named William and I'm his friend. No need to tell me twice._

_ Good now go to sleep._

_

* * *

_**Sorry if that huge telepathic conversation was a story killer.**

**I don't ship Amy/11 by the way so don't expect anything.**


	3. Detective's Hunch

The next day, Amy woke up and for once, she missed the sunlight splashing her face. She'd often found it annoying to open her eyes and be blind. Even the TARDIS did that to her, as if it wanted to tease her. In this dark world, however, sunlight was welcome. Turning, over, she saw the Doctor sitting on the edge of his bed. The candles illuminated the room.

"Rise and shine," he teased and tossed her toiletries that were sent by Rhea one hour ago. "Clean up and wander around the Silo. Don't get into any trouble; don't do anything stupid and don't offend anyone."

"I won't," grumbled the Scottish girl.

"I'll be working."

"Alright." Amy brushed her hair with the brush that was given to her. _So basically, you want me to snoop around._

_Don't make it too obvious._

_I know._ "So how come your hair's all neat and everything?"

"I'm just magnificent like that. I'm going now. _Don't_ do anything stupid."

"I won't," Amy repeated. "Mr. Grumpy Face," she muttered under her breath as the Doctor left the room.

* * *

"Good morning all!" the Doctor exclaimed as he marched right into the Torchwood base. "Hopefully the sun is shining outside. Now, captain sir! What did you want me to do?"

David handed him a case file. He was ginger with freckles splashed across his face. "The control room you saw below one level is hooked up to the transducer but the whole system's been offline for a month. There was a lightning storm. Cut off the power supply."

"Great, where?"

"There's a damaged area in the west wing of the Silo. And-"

"Wires need a bit of reconnecting, booster needs a touch-up. Easy job." The Doctor studied the diagrams upside down. "Easy job. Long job."

"I could send you someone," Harkness offered.

"Naw, that's alright. More of an individual worker. Now if you don't mind?" The captain nodded and the Doctor scurried off, heaving a breath of relief to get out of the man's presence.

* * *

Amy walked around with her hands in her front pockets. Her right hand poked at the TARDIS key the Doctor had given her earlier. Maybe this was one of those times where she should wait in the TARDIS until it was safe. She'd do it but it was too dangerous outside.

Snooping around was thrilling too. Amy felt like she was in one of those James Bond movies. Except that she was a girl, and that this wasn't the 21st century. There seemed to be a lot less guns in the picture as well. Turning the hall, she found the halls were all the survivors were gathered. They regarded her with interest. Her clothes were different and on top of that, she was clean. Her eyes did not look sleep deprived like the rest of the people.

A ball rolled up to her and Amy bent down to pick it up. A little boy scurried up and whispered a hasty "sorry miss" before hurrying away. Amy smiled and sat down next to a woman who looked no older than she did.

"Hello," Amy greeted.

The woman looked at her and glanced away. "Hi."

"Amelia Pond," the Scottish girl introduced. "Or just Amy." She stuck her hand out. When the woman didn't shake back she dropped her hand embarrassingly. "What's your name?"

"Emily. Emily Hodges."

"I had a mate named Emily once. Back in Scotland. Ages ago. Really… ages ago."

"What happened to her?"

"We… drifted apart. I moved away."

"We lose so many people these days."

"Yeah," Amy agreed, thinking about her mother and father. She glanced around at the other people who still eyed her warily. "Blimey, they're all still staring at me."

"You and that friend of yours have been the talk around here the whole night. It's like the two of you haven't seen the war. Clothes are clean, face is clean."

"It's a long story," Amy explained. "And I'm not supposed to tell."

"Being secretive makes you a target."

"So how come you're talking to me?"

Emily shrugged. "I guess it just seems I can trust you. I feel like I can. My mum used to say that I had a knack for knowing things."

"Like strong sense of empathy?" Amy supplied, smiling and nodding.

"I suppose so. Tad would disagree."

"Tad… You're a Welsh girl aren't ya?"

"Yes."

"So how did this all happen? I mean all the mutants I mean."

"No one really knows the details. All we know is that there were these scientists experimenting on humans."

"Isn't that illegal?"

"Not anymore. Where have you been?"

"Ah, bit of a traveler."

"They were developing a new drug. It was supposed to some kind of immortality elixir."

Amy actually laughed out loud. Her laughter was lost in the noise of the busy corridor. "That's what I thought too," Emily told her. "Immortality is impossible. But those poor people. Once the information leaked to the public, people began to protest. Eventually they were released and started to attack everyone."

"War broke out then," Amy finished. "I remember that," she added for good measure.

"That Torchwood group, gives me the chills."

"Oh really?"

"That leader one, he's hiding something. He keeps saying that we'll blast them out of the sky. Giving us hope. He doesn't believe it though. One time, I was wandering and I came to this dead end but it was a dead end. I saw the door. And I tried to open it. In an instant that captain was beside me. Guided me away. He seemed livid."

"Where's the door?"

"You won't be able to see it. Everyone else said they went down that way all the time but never saw it. I'm not dreaming; I know I'm not. I saw it. I swear."

"I believe you," Amy said honestly. "I'll go see it for myself. Just tell me where it is." Emily reluctantly revealed which hallway. "Thanks," Amy said, giving Emily a small hug. "Nice speaking with you."


	4. Unraveling Lies

Amy was careful not to be discovered, even though she knew cameras were all over the place. It was the 31st century. What other technologies could allow others to be spying on her? The Scottish girl walked around like she owned the place, not like she was snooping. It might have been what the Doctor said, but in her mind she was "exploring." Her excuse was that if she was going to be living here, she might as well know what the place held and what it looked like. Didn't want to get lost in one of the halls did she?

She arrived at the dead end Emily had detailed to her about. There was nothing there. Amy rolled her eyes. Had she really just wasted her time? Turning on her heel to walk away, she suddenly remembered the Doctor's words. _Notice everything… Look… exactly where you don't want to look, where you never want to look. The corner of your eye. Look behind you._

Pretending that it was her house on Earth in the 21st century, the second time she'd met the Doctor, Amy turned around slowly. And she saw it –barely. She knew it was there; she could make out the rough shape, but it was blurry. Her eyes couldn't focus. Slowly, she made her way the door. Amy saw a shadow move behind it as she approached. Looked alien. But what was it? Curiosity won her over as she pressed against the door.

"What are you doing here?" someone asked.

Startled, Amy spun around to see Captain Harkness staring sternly at her. "Oh, you know… Just exploring."

The captain visibly relaxed. "This is off limits."

"Sorry, didn't know."

"Be more careful next time. Come on. You're friend William is waiting for you."

* * *

Amy let herself be led back to the main Hub of the Torchwood underground facility. The Doctor sat in a chair, hands nervous and staring at a screen. His eyes skimmed from left to right as he examined old readings. "Mad…" Amy heard him mutter.

"Will?" she ventured.

The Doctor turned around and held a hand up. "Hold on." He gazed back at the screen and back to Amy. "Hello Amy."

"Is there something wrong?" Harkness questioned.

"He's been like that ever since you went to fetch Amy," Miriam laughed. "He came in through door demanding to see records of everything that's happened here in the last month."

"Like I said," Harkness reiterated, "is something wrong?"

"Not wrong," the Doctor clarified. "Just missing. Like a crack in the wall. Like a memory. The puzzle pieces don't fit together."

"So what's the missing piece?"

"Connection gets frazzled, wires burn out. Thin wires, relative to say… power lines that power one of those old nuclear power stations. But the energy that would be coursing through would overload the entire system. Cause a meltdown."

The captain looked scared. Not scared in horror, but scared in a way where a child is caught with their hand in the cookie jar. He schooled his features before anyone but the Doctor could notice. "Then what can we do?"

"Searching through the records for anything out of the ordinary. Besides that strike, you haven't had anything else have you? No abnormal weather, infiltration…"

"No," David called.

The Doctor yawned. "Alright. I'll go check out the interior of this place if you don't mind. Don't want to end up with some accident. I think a survey of the premises would prove wise?"

"Of course," Harkness agreed. "Go on."

"Amy, would you come with me?"

"Oh, yeah sure." Amy responded absent mindedly.

The two of them walked out into the hall and kept up their façade while Amy recounted the events of the morning with the Time Lord through the mental link. Periodically, the Doctor would pause and check the walls or circuitry. More than once he pressed his ear up against the metal plates surrounding them.

Then they reached the dead end. Their backs were to the camera, preventing the video tape from showing the Doctor's unnerved face. "Well that's boring," he managed to splutter out. "Dead end." Amy couldn't help but feel that sudden change in the atmosphere. It was like someone took a live cable and shoved it in her face. What could make the Doctor so stiff? "Come on Pond. Let's go."

She'd have to ask later.

* * *

The night was colder than usual, but it could have just been Amy's nerves. _What's in that room?_ she asked the Doctor.

Across the room, the Doctor lay still, his back towards her and eyes closed. _Nothing._

_How old are you again?_

_ 907._

_ 907? That's a lot of time to practice lying. You're still bad at it._

_ That's just recent._

_ So what's behind there?_

_ An alien. Crying out for help. Hurt, in pain. Aching and dying. It's a hostage._

_ One of the mutants?_

_ Oh Amy Amy. Amelia Pond, the girl who waited. The girl with a fairytale name and then grew up. This war is a fluke. It's all so ironic on so many levels you don't understand._

_ What is it Doctor?_

_ Those mutants, isn't obvious? From the moment you saw them when you met the Captain, they were human. Human all along._

Amy nodded. _I know. Emily… Hold on. I _knew_ they mutants were human. How come I never ques-_

_ That's the perception filter messing with your mind. This whole underground oasis is filtered with some telepathic signal. Keeps the people from questioning. That _room_, high level perception filter. Only those specifically trained can see through it._

_ And behind the door is the real threat?_

_ Yeah. I should have known he'd do something like this… too old me. Too old, too thick-headed._

The urgency in the Doctor's thoughts troubled the ginger Scottish girl. _What is it Doctor? What's really wrong?_

_ The energy? And the readings I was looking at? The moment that transducer powers up the plant and shoots something to destroy that ship, the whole lower deck gets flooded with radiation. The people die, disintegrate before then even know what hit them._

_ That's murder,_ Amy stated blandly.

_The cables aren't designed to carry that much energy. The only safe place here is that main Hub and it barely fits fifty people. And those people down there? Probably thousands._

_ So we stop it._

_ If it were that easy, we would already have left.__

* * *

_**Another killer telepathic speech? Yeah, sorry.**


	5. Nonexistent Hostage

**Just to let you know, the Jack in here is post-CoE. If you don't watch Torchwood, things might get a little confusing.**

**That little hint also helps with the mystery in the next chapter.**

**

* * *

**

The Doctor actually fell asleep that night. It'd been a while since he'd last slept, or even dreamed. Sleep did not come to him naturally. Maybe it was one of the perks of living too long or traveling too much. Time zones didn't matter after a while. The Time Lord knew another man who didn't sleep much either…

Dreams. Right… dreams. Dreaming. Doctor hadn't done that in a while as well. Even when he did sleep, dreams didn't come. But this dream, it was a nightmare. The Doctor flinched as he felt an orange light blaze past him. The world was in ruins; buildings were burning –the world was one fire. The world… was _burning_. He flashed from place to place. It was suddenly dark, there was a cry. He ran. He ran as fast and as far as he could. Suddenly, he was looking at a rocket. Then he was on a posh flight deck. He was back on the Earth again.

He was the last one standing.

Behind him was an ethereal light with just the tint of blue to the white. He squinted. It was smiling at him. The light was _smiling_ at him, smiling like a crack. It was engulfing him, pulling him down. The Doctor tried to glimpse his changing surroundings. The Death Zone.

It was the Death Zone and he was playing the most dangerous game in all of time.

"Will!" It was a hiss as he felt a slap across his shoulder. Jumping awake, he hit Amy's forehead on accident.

"That's what I get for waking you up," pouted the Scottish girl.

The Doctor rubbed his forehead and winced a bit. "Sorry," he apologized.

"Care to explain your sudden attack?" Amy joked. She had a playful smile on her face. The Doctor however, did not look amused.

"You know when you try to forget something…" the Doctor began, fully aware of the cameras and voice sensors, "and you think you've pushed it to the back of your mind, but it suddenly unlocks again?" The Doctor got up and snapped his fingers. "Just… like… that."

Amy raised an eyebrow at the cryptic words. "I'll pretend I understood that."

"Anyway," sighed the alien. "I'll need your help today. Care to lend me a hand Pond?" He sprinted out of the room but before Amy could follow, he popped his head back around the door. "Not literally, though that _has_ happened before."

* * *

The Doctor and Amy walked into the man Hub to find David and Rhea arguing. David, who was the medic, had a scalpel in his hand. It was a fancy, futuristic scalpel by the looks of it. However, the Doctor really didn't think that it was safe to be waving that around whilst angry. He suggested that David set it down first. That earned him a glare.

"Please?" Amy asked sweetly. David gave a softer glare but set down the scalpel.

"Is something wrong?" inquired the Doctor. Rhea began to speak but David shushed her. "Well seeing that the two of us are helping you, we'd like to know what's going on."

"We received a message," Rhea said. David groaned and tried to step out of the conversation. The Doctor, who's arms were previously crossed at his chest, reached out with one hand and grabbed David back.

Without leaving his eyes off the blonde in front of him, he asked, "What kind of message?"

"Well, the aliens –those mutants- they've been taking the humans, just random ones off the street."

"Hostages," remarked Amy.

Rhea nodded in agreement. "They want to exchange hostages."

"So?"

"So we haven't got a hostage!" David cried.

"And they think you do?" questioned the Doctor as he raised an eyebrow. Rhea nodded and the Doctor quickly glanced around. "Where's the Captain?"

"Patrol, something like that," muttered David. "He's with Miriam. The message just came in."

"So why don't we start from the beginning?" suggested the Doctor. "Mutants are the aliens and their attacking." Rhea and David both confirmed that. "Okay, what do they want? What's their purpose?"

"Resources," David answered.

"What kind?"

"I don't know. Food, water, energy?"

"Planet of origin?"

"Untraceable."

"So they're here, but they want something…." Amy trailed off. "So why pick Earth? Or New Earth," she added on quickly.

The Doctor paced quickly, muttering softly. "Traveling distance, traveling distance… 600 planets fitting the descriptions…"

"What is he saying?" Rhea asked, leaning over to Amy.

"He's a bit weird like that," Amy replied. "Just don't worry about. Oi Will!" she called. "Think in your head!"

Just then, the Doctor stopped. He walked over to the three humans again, who'd gathered around a counter. The Time Lord laid one hand flat on the counter, the other making a vertical motion to the surface. "Ah ha!" he cried. Amy jumped back. "You know how it's like when you get bullied?" the Doctor began. "Maybe some kid wants your money or something like that. The first time, you say no because you want to be brave? Then they pick on you. The next time, you give them the money because you know better, you know what happens if you don't."

"So?" Amy asked with a tone.

The Doctor's eyes sparkled and gleamed. He debated on explaining before Harkness and Miriam came back into the door. Turning around, he greeted them cheerily and pulled Amy out as he excused them to go work on the transducer.

The arrived at the control room where the Doctor explained that he'd already hooked up the wires correctly. _I need to override the protocol,_ he explained silently. "Flip those three switches right there," he ordered, pointing at the control panel to his right. He was currently on the computer, scanning through the records.

_What are you going to do?_ Amy asked.

_Transferring control to my sonic screwdriver. I just need to send a signal._ The Doctor grimaced. "Layers of code to figure out. Magnificent…"

* * *

A little more than half an hour later, Emily was trying to find the lavatory installed in the Silo. She'd only been here for a while so she often got lost. It explained why she found that room that no one could see and enter. The Welsh girl wondered if that newcomer Amy had found it. She probably didn't. No one could see that room. Emily was even convinced that she was crazy. It must have been the air outside messing with her head. Pollution levels were horrible to begin with.

Just as Emily finally found the lavatory, she looked to her right.

She screamed.

**The Doctor's dream sequence is supposed to reference the Pandorica Opens/The Big Bang... or something.**


	6. Premonitory Death

Amy rolled her eyes as the Doctor attempted to get past what he called "intricate layers of Torchwood security codes that should not be majorly changed in order to prevent a paradox or something bad like that." The engaged Scottish girl knew that it was the Doctor's way of saying "it's hard." If there was one thing that she'd learned about her imaginary friend, it was that he had a ego possibly the size of the TARDIS's interior.

"Doctor…" Amy sang impatiently. "Are you done yet?"

"No, not really. Almost."

"You said that about ten minutes after you started. Do you even need me for anything."

"Pond," the Time Lord began, turning around. "Be quiet."

Amy rolled her eyes again and let out a sigh this time. Checking her fingernails, she leaned her hand on the Doctor's chair. _Honestly,_ she thought, _how long does it take?_

_If I do a clean download all at once, someone's going to notice. I'm almost done, promise._

_ How long?_

_ 25% to go._

That's when the scream came.

Amy's head whizzed up. "What was that?" she asked, fear evident in her voice.

The Doctor looked up too and quickly locked the program he was on. Standing up, he whispered, "I don't know." Then he bolted out the door with his companion quickly trailing him. They stumbled to a stop as they came behind Emily.

At the same moment, the Torchwood team appeared opposite of them –right behind the thing that made Emily scream.

The Doctor slowly approached as he pushed Amy behind him. "You alright?" he whispered to Emily. The girl sucked in a shaky breath. He nudged her back to Amy and continued to approach the creature carefully. It was facing his way, possibly oblivious to the team behind him who all had their guns poised and ready to shoot.

Harkness cocked the gun. "Don't," hissed the Doctor.

"It's a threat," the captain replied.

"Don't," he repeated, hand outstretched in objection. He kept it there as he approached again. The creature stared oddly, but slumped to the floor. "You're hurt," the Doctor stated. "What are you? Where are you from?"

"It doesn't understand English," the captain interjected.

"Quiet!" the Doctor snapped. He looked back at the creature. "Alien I assume?" His voice was soft, like a father comforting a daughter. "Lost? Did you crash? How did you get into the Silo?" The alien obviously did not reply. The Doctor stretched his hand out more. "Can I touch you?" He reached out and almost brushed the skin of the alien. This time it responded by lashing out. The Doctor jerked back and saw the Torchwood team jump. "It's alright," he continued. "I won't hurt you see?" The called back, "Amy come here."

"Why?" she asked, scared.

"Come on Pond."

The girl slowly approached and the Doctor touched Amy's hand. "See?" he said to the alien. "Perfectly safe. No poison or any nasty stuff." The Doctor tried to reach out again. This time he was met with no resistance. "It's going to be alright," the Doctor smiled. "Now what's wrong?"

As soon as the Time Lord had gained the mysterious alien's trust, that trust dissipated. The alien lashed out again, this time sending the Doctor tumbling back in surprise. Amy backed away as well, but the alien advanced on them. The Doctor could see the captain, wavering with is gun, his finger threatening to shoot.

"No!" the Doctor shouted, but it was too late. Bullet met flesh and the alien fell down lifeless. The Time Lord sprang up, enraged. "What was that for?" he yelled. Amy stepped back to Emily. She had never seen the Doctor so angry, except for their visit to Starship UK. But that was more of an agitation –the agony of choosing. This situation, however, was different. The Doctor was truly mad. No, scratch that. He was _livid_ at the captain for shooting.

"What was that?" the Doctor yelled again.

"It was a threat," Harkness said, maintaining a straight face.

"It was scared. It was _defenseless_."

The Doctor strolled right up to Harkness, Miriam, Rhea and David. Right in their faces, he whispered, "I've got a thing about guns." Then he turned the other way to return to the control room. "Come on Pond."

* * *

On their way back to the room, Amy did not utter a sound. That was because she was preoccupied otherwise. _Explain_.

The Doctor did not reply at first. Amy noted how the Doctor was starting to do that often. _Who is he?_ she followed up. _What was that?_

_An alien._

Amy resisted the urge to whack him on the back of the head. _Obviously._

_ It's what was in that room._

_ How did it get out?_

_ Not our concern._

_ You said it was scared._

_ Would you be if you were it?_

_ I need you to stop and tell me what's wrong,_ she demanded. She stopped walking and said out loud, "What the hell is going on here?"

The Doctor looked passively at her.

The alarm bells rang. Amy groaned. "What is it this time?"

The Doctor looked up at the ceiling. "The mother ship is here… and they want their hostage."

* * *

**-cue dramatic music-**

**Dunh, dunh, dunhhhhhh.  
xD**

**I'm having a hard time thinking of two word chapter titles. T_T**

**On a brighter note, anyone else totally HYPERPSYCHED for the Series 5 finale? I AM! **


	7. Falling Ash

**First off, I'd like to thank everyone who follows this story and reads it. I turned to check my email today and there were 14 messages of favs/alerts etc. Thank you guys so much!**

**Here's the moment you've probably all been waiting for. The Doctor vs. Jack.

* * *

**

Rhea was readying herself at the controls, ready to accept the transmission. Miriam sat at her desk, fingers poised on the touch screen computer. She'd been tasked to trace the signal. And David… well David stood around and just watched. He saw his boss fidget nervously with the button on the control panel. The big red button. Fire.

"Incoming transmission," Rhea reported.

"Open line," the captain ordered. Rhea obeyed and the static filled image of a mutant appeared on the screen.

"They've deadlocked their system," Miriam whispered. "I can't tell much, only that they haven't entered New Earth's intergalactically set airspace borders."

"You will give us what we require," the mutant commanded.

"We're not handing over any resources," Harkness said steely.

"We do not require of that at the moment. We have hostages. We will offer a peaceful exchange if you comply."

"We don't have a hostage," David called out.

"We scanned your planet. The coordinates lock onto your facility. We detected a life form of ours."

"Your hostage is dead," came a firm voice from the doorway. Torchwood turned their heads to see the Doctor leaning on the doorway with Amy Pond standing next to him. Her arms were crossed and she put the weight of her body on right foot. Together, they looked like a secret agent team, just without the fancy get up. In a way, they were secret agents –self-employed of course.

The Doctor pushed off from the doorway. "Scan again. There isn't a hostage."

"Where is our hostage?" demanded the mutant.

"I told you it was dead," repeated the Time Lord.

"This is my negotiation William," Harkness argued as he came up to the Time Lord.

"You can't go on like this," the Doctor simply responded. His voice was deadly, as if it could set off the sequencer and shoot the beam at the spaceship in the sky. His eyes, however, were passive and directed straight at the captain. They looked right through him. "If you blow that ship to kingdom come, you _disintegrate_ every survivor down there."

"Will, you aren't the one in charge around here. You may be smart, but this isn't your war."

"And it's yours?" exclaimed the Time Lord. He gestured at the rest of the team. "Is it _your_ war or Torchwood's war? What's the rest of your team got to say about it?"

"They don't know what else there is to do."

"Then why don't you tell them the truth?" challenged the Doctor. Silence followed. "Why don't you tell them what's really going on? Those mutants aren't a race and you know that very well. They're exactly what they are. Just mutants. Why don't you tell them who's really behind the attack?"

"I don't know what you're talking about."

"Yes you do."

"How do you even know this information?"

"Perception filters don't work on me. Even high-level ones. I'm more perceptive than you think I am. I _know_ what that was in the hall. I know it's what they wanted. And I know who _they_ really are."

The mutant on the screen began to speak again. "If you do not have a hostage, then we are forced to reconsider. You will give us the resources or we will rage war."

"That's against the Shadow Proclamation," Harkness pointed out.

"The code states that it is illegal to rage war with a planet that has done no harm. If you have destroyed our kind first then it is not against the Shadow Proclamation to start a war. You will give us the resources."

"No deal," Harkness replied.

"You must reconsider," mutant number one replied. "We have this in our possession." The camera panned to the right and revealed a blue police box.

"What is _that_?" David asked.

Amy cast the Doctor a worried glance. The Doctor then sneaked a peek at Jack who met his eyes in an instant. In less than a moment, Jack had his gun drawn on the Doctor.

"Jack!" Miriam cried, but the captain ignored her and kept his steely gaze on the Doctor. He cocked the gun.

"Captain," the Doctor warned calmly.

"Give me," Jack began, his voice barely in control, "one good reason why I shouldn't shoot you in both hearts and in the head to make sure you die?"

"What the hell are you talking about?" David yelled.

"Doctor, what's happening?" Amy whispered in fear.

"You were on the right track when you talked about River. Old friend," the Doctor replied, "companion and um…"

Jack shot twice on the floor in front of the Time Lord and raised the gun up again. "Third time's a charm Doctor."

"I'm not going to stop you from shooting me. Just give me three minutes to talk," negotiated the Doctor. "Because you know me, talk too much whatever I look like."

"You can't convince me of anything and no I don't forgive you," Jack spat.

"You won't shoot me Captain," the Doctor commented.

"How do you know that? I've changed a lot over the past centuries. I'm not the same person; you don't know me anymore." Jack gripped the gun even tighter.

"Centuries?" Rhea raised her eyebrows.

"But I do Captain," the Doctor continued. "I know you won't shoot because you're just like me. Always walking, always wandering. Always hoping. If you pull that trigger right there, then the only person you can ever hope to relate to, me, wouldn't be around anymore." He held Jack's gaze, tempting him to shoot. "I'm sorry. I'm so so sorry. And I'm truly am with both of my hearts. It was a fixed point."

Jack gulped and fidgeted, the gun wavering in his hand. Finally, he moved his arm, but the Doctor sensed what he was doing. "Captain, don't!" It was already too late. Jack shot the bullet in his head.


	8. Reconciling Absolution

**I now feel no qualms about using the name "Jack" in the story.

* * *

**

Jack's team each reacted in the same way –they screamed. Amy just jumped back, already at a loss for words. "Magnificent," the Doctor muttered, kneeling by Jack's body. "Just bloody magnificent. Amy! Get a rag or towel and be quick about it. Clean up the blood."

Amy's face turned a bit green but obeyed his orders. The Doctor got up and faced the transmission screen. "Well that was the show. I hope you enjoyed it. Now where were we?"

"Wait!" David called. "Jack is dead. I'm second-in-command. You're in no position to negotiate."

"See the thing about Torchwood is that you are always about the etiquette. We're at war! Besides," the Doctor shrugged. "He's not going to stay dead for long."

"How do you mean?" Amy asked, wiping the blood from Jack's brow.

"Something that happened a long time ago. He can die, but doesn't stay dead. He's immortal."

"That's not possible!" Rhea declared.

"But why wouldn't he tell us?" Miriam added.

The Doctor's usually happy demeanor clouded over just a bit. "Stuff happened."

"You will hand over the power supply," the mutant called from the screen.

"Oh yes!" the Doctor cheered up in an instant, "Right! Sorry. The answer is no. Zilch, nada, nope, invalid."

"Then this world will crumble."

"But here's the thing. You're acting from higher orders aren't you?" The mutant did not seem amused when the Doctor uttered those words. "Because honestly, you're just a bunch of human mutants. You think that you deserve better treatment than what those meanie scientists gave you and now you think that all the others humans are like that. So therefore when you broke out, you attacked everyone else. In turn, you became guilty of crime and everyone turned their guns on you.

"Those scientists didn't make you super intelligent either. Nope. The smartest creature out there is still me. So show me, who's the big boss I am supposed to beat?"

The image shook and displays of TV static startled the screen. Radio static could be heard as a new alien filled the screen. The Doctor, who'd been leaning with his hands on the table in front of him, pushed from off the table. He never once took his eyes off the screen.

"Rhea, Miriam, David," the Doctor called gently. He paused in between as he said each of their names. "This is the reason for Jack's willingness to sacrifice the survivors."

"What _is_ that?" Rhea spat.

"Nyalaxo, more commonly known in Earth's history as a 456."

Amy's eyes went wide. "You don't mean-" Her question was cut off as Jack came alive in her arms, gasping. The Doctor tried to ignore the immortal for a while longer.

"You want the energy supply because you're dying. You're weak!" the Doctor laughed.

"Then we just blow them out of the sky!" David exclaimed.

The Doctor looked back with a disdainful face. "That's very Torchwood of you isn't it?"

"They're a threat."

"Doctor please," Jack whispered. The Doctor looked down at his age-old friend. For a moment there he wondered. He wondered what horrors those two human eyes had beheld. He wondered if the things Jack had seen were more terrible than his own. He wondered if it was worse than watching your planet and your people be consumed by time.

The Doctor took a breath and put in his serious mask. Returning his gaze to the screen, the Time Lord said, "You were refused centuries ago and you've fell out of time into the future through a crack. Your supplies are low and your species' flawed addiction is killing you. I will give you a choice. Leave this planet and its people and find someplace else or there will be consequences."

"You will give what we request."

"Just as I thought!" the Doctor declared. "Well then. Bye!" He whipped out his sonic screwdriver and aimed it at the screen. The transmission was cut immediately. He looked at the captain who'd regained his composure and was trying to avoid the gazes of his team. "We've got a bigger problem now," the Doctor told Jack.

"So blow them out of the sky."

"The people Jack!" the Doctor shouted. "What about all those survivors?"

"A small price to eliminate a threat."

"The Captain I knew wouldn't say that."

"I told you. I've changed."

Jack turned on his heel. "Don't walk away," the Doctor started. "Don't you dare walk away Jack!"

"Doctor!" Amy hissed, trying to hold him back. The Doctor broke free of the Scottish girl's grip.

"You've given them _hope_ Captain! You've called this the _Silo_ and promised them _Utopia_ but you're no better than _him_!"

The Doctor knew that would catch Jack's attention. His hunch was confirmed when the immortal turned around and strolled up to the Doctor. He landed a heavy fist on the Doctor's jaw.

The Doctor fell back muttering, "Suppose I deserved that."

"Don't you dare!" Jack shouted. "Don't you dare compare me to him! You know what he did to me! What he did to Earth!"

"Then prove to me that you aren't like him."

"There's no other way."

"Jack, Jack, Jack. There's always another way."

"There wasn't that many years ago."

"There's mostly always another way," amended the Doctor.

"This is one of the exceptions."

Jack started to walk away again, but the Doctor uttered two more words. "Bad Wolf." Jack turned around again. "The first time I ever heard that was on a ship above a burning Earth. That was the first time I saw you in the future. Didn't know it was you though. You looked _so_ different." The Doctor approached Jack slowly. "Then, second time I saw you, I was with Rose again. Stuck on New Earth. Not this one though. The 15th version. Didn't know it was you either. Third time, still didn't know it was you, yet. I was with Martha then. Oh but you were magnificent. Brilliant. Fan_tas_tic. Want to know what else though?" The Doctor was nose to nose with the ex-Time Agent. "You. Died."

The Doctor could hear Jack's breath hitch so he walked away and made a show of waving his hands around everywhere. "That's right! You died. Nothing ordinary there right Jackie boy? But!" He pointed. "You didn't come back. You died saving the human race. Isn't that just fantastic? Brilliant? Magnificent? So." The Doctor leveled his eyes with Jack's. "Now you know that you're going to stay dead one day... You know you'll see everyone again. What's the plan now?"

Jack was impossibly silent for a while. Many in the room thought he didn't know how to speak anymore. "Some other way," Jack finally choked out.

The Doctor grinned. "Geronimo!"

* * *

**I feel like I've butchered Jack's personality with this story. If I have, then my lame excuse is that he's had a lot of time to become a different man. As our lovable Captain so states he's "changed."**


	9. Political Chatter

The Doctor grinned wickedly. "Aye aye captain!" he began as he started to pace the floor and ramble. "If they sent a long range transmission then it means there're a way off. How far though?"

"We couldn't trace it," reported Miriam.

The Time Lord whisked out his sonic screwdriver and aimed it at the computer Miriam was sitting at. "Falling out of time, engines failing. Extra stain on energy using deadlock technology. I'd say maybe 20 minutes away? Yeah, less half an hour and no TARDIS. Perfect, déjà vu. Oh it feels good to ramble!" he declared. "Does time always pass that slowly, in the right order?"

"Who _are _you?" David demanded.

The Doctor straightened his jacket. "I'm the Doctor, the Oncoming Storm. And before you ask, yes. I _am_ an alien."

"Doctor who?"

"Just the Doctor," Amy answered for him.

"Half an hour and they've deadlocked most of your system. Which means this-" The Doctor held up his sonic screwdriver. "Which mean's this is risky."

"How do you mean this?" asked the Scottish girl uneasily.

The Doctor pressed the button and the tip glowed green. "They've got your weapons set on self-destruct."

"You said you transferred 75% onto your screwdriver though."

"Like I said, risky."

"If you don't mind me asking," interjected Rhea, "what was that out in the hall?"

"Your hostage. Rule number, always expect the worst. They weren't going to accept a friendly exchange hostages. First off, they'd use humans they kidnapped. Didn't you notice they were all children? I'm sure the Captain did. The Nyalaxo were going to steal the resources and destroy the planet."

"You said it was scared," whispered Amy.

"It was in unfamiliar terrain. Of course it was scared. I tried to reassure it when I touched it, telepathic link. Common trick. I must have accidently thought about…" The Doctor trailed off and met Jack's eyes. "Anyway!" he clapped his hands together.

"You have a plan?" questioned David.

"It's a Thing, not a plan. It's better than a plan. Anyone know if there's a teleport around here?"

"No!" the medic snorted.

"Oh right, sorry. First successful wide-ranged teleport is 4167. Wait a minute!" The Doctor held out his hand to Jack. "Wrist strap."

"Hell no!" he replied defiantly, even going so much as jerking away. "I'm not having you fix it only to break it again."

The Doctor checked his watch. "12 minutes, world at stake." The captain reluctantly forked over his Time Agency vortex manipulator. "Benefits of having technology two millennia ahead of the times. Just need to adjust it for those terrible headaches. Remember last time?" the Doctor babbled as he took the sonic screwdriver to the strap. He shot a quick look at Jack. "Circumstances were a little different. Still, Silo… Utopia… Well then. Wish me luck." The Doctor smiled. "Geronimo!"

* * *

The aliens immediately knew that their security had been breached. In fact the 456 leader turned around immediately and called for its mutant soldiers. "How did you breach the ship?" the leader demanded.

The Doctor laughed and threw his head back, leaning on the TARDIS that he so happened to materialize next to. "Oh, saving the world never ceases to amaze. And that's not a bad thing either. Otherwise, it'd get boring after a while."

"Stop this talking now."

"Do you know who I am?" Silence.

"We demand planet of origin."

The Doctor laughed. "So you _don't_ know who I am. The Doctor by the way. Not Doctor insert-last-name-here. Just, the Doctor."

"We demand planet of origin."

The Time Lord smirked. "Gallifrey."

"A legend on its own. A myth."

"Oh thank you. That's very humbling. Now here's the choice. Leave and never come back or suffer the consequences."

"We refuse."

"Ha ha," the Doctor chuckled. "Thought so. Don't say I didn't warn you. I gave you a choice."

"You will meet our demands."

"As I said," ignored the Doctor. "I'm the Doctor. And you know who's down there on New Earth? That's right, Captain Jack Harkness." The Time Lord searched for any sign of recognition on the alien faces. He concluded that the Nyalaxo had very good poker faces. Then again, their face wasn't composed of much facial muscle. "Jack Harkness. You know him. 1965, gave you 12 children. 2009, fought you? And I'll tell you what, it hurt. Really hurt. Now normally I don't believe in mass killing or genocide, as Jack is trying to convince me to commit. So I'll ask again –nicely I might add- will you please leave?"

"Why are you loyal to him? You have more power and potential."

"Power? Maybe," the Doctor agreed. "Potential? Not so quite. Because that's what I like about humans: such a short life span, so many ideas."

"Why are you loyal?"

"Need there be a reason? 'Cause he's friend. There's nothing wrong with lending a hand is there? Although, not literally of course. Just once though… And, right! Where was I? Please leave. Thank you very much."

"You have our answer. Now you will be executed." The mutants raised their weapons as if on cue.

* * *

**I'll be posting an outtake at the end. I write by jotting down scenes that come to me. Then I fill it in and realize that scene won't fit in the plot. So yeah, deleted scene at the end!**


	10. Vesuvius Erupts

"Wait," the Doctor said calmly, holding up a finger. "You, what's your name?" He pointed at the mutant right in front of him.

"I have no name. I am just Subject 353836"

"You're still human. You had a name. What was it?"

After some hesitation, the mutant said, "Marc."

"And you?" the Doctor asked the mutant to the right. "What about you?"

"Subject 362837."

"Name."

"Antony."

The Doctor raised his eyebrows. "He's Marc, and you're Antony?" They both nodded. "Good good good!" the Doctor exclaimed. "Because you're still human. Maybe you don't look the same, but you still are. Look around you; look at what you're doing. You're about to aide in destroying an entire race. _Your_ race. Come with me. I can help you get a better life. I can clear up the controversy. I have so friends willing to help."

The Doctor could see the hesitation in all of their eyes. "There are more of you on New Earth. You don't have to hide out anymore, doing dirty work. Come with me. Really."

"You will cease this blasphemy!" the 456 leader ordered.

"I'm sorry; do you know who I am? I've already explained this. I'm the Doctor, the Last Time Lord. I'm the Oncoming Storm, Karshtakavaar, Ka Faraq Gatri, the Lonely Angel, Time's Champion. Look at yourself. You're a three headed slimy alien that needs to be kept in a certain gas-filled chamber to survive. Do you honestly think you can defeat me?"

One by one, the mutants started to line up next to the Doctor. The Time Lord smiled victoriously. His glory was short-lived when he realized what was to come next. "Get in, get in!" he urged as he snapped his fingers and pushed the mutants into his TARDIS. He closed the door after himself and made a desperate dash for the controls. "Bigger on the inside," the Doctor rambled desperately. "That's all I have time for. Seven minutes until the end of the world."

* * *

"Okay then…" Amy smiled as she clapped her hands together. She looked at the black screen. The connection had been cut. That meant she didn't have a way of contacting the Doctor at the moment. They would be able to know what was going up there. In truth, she wasn't worried about the Doctor as much as she was worried about herself. She'd seen the Doctor. He could work himself out of any pickle. In fact, that had just been proved wonderfully by the recent encounter with the Weeping Angels. Thinking about them still gave Amy the chills.

No, she was worried about herself because the Doctor had left her in a very awkward position all by herself. "So…" she trailed off. Silence fell right after her.

"If it helps, I'm too confused to even say anything," David quipped.

"Is now the time for sarcasm?" Amy rolled her eyes. She leaned against the table. "We should be worrying about if those missiles you lot have will detonate on us."

"They're leaving," Miriam reported.

Amy looked over. "How'd you tell?"

"Residual trace of the transmission signal. It's getting weaker."

And to Amy's delight, she felt an invisible breeze and the sound of the TARDIS materializing with its brakes still on. She turned around and saw the police box, grinning. However, the Doctor was not as ecstatic. He pushed past his companion and immediately launched himself at the controls. He was a frenzy, just like when he was piloting the TARDIS through a rough spot in the time vortex.

The mutants stumbled out too, completely taking everyone by surprise. "When this is all over, they'll be treated like every other human out there. Is that understood?" The Doctor was met with no voiced complaints. "Good. Now, how long have I got?" He looked at his watch. "Five minutes until New Cardiff explodes. Very not good indeed."

"What's wrong?" asked Amy.

"They're detonating the missiles and your systems are still deadlocked. I can override it if I can completely transfer the signal to my screwdriver, but that'll take five minutes at least!"

"Well then do it!" Amy yelled.

The Doctor whisked out his screwdriver and started to download the remaining quarter percent as a clean download. It was trying his patience. Soon, two minutes were left. To his surprise, the download completed and he stuck his screwdriver in a port, not caring if it was compatible. Everyone held their breaths as the screen filled with the countdown for detonation. Amy crossed her fingers. At the last possible second, it stopped and systems were back online. However, the whizzing of the missiles were still heard.

"What's going on?" Miriam asked, afraid.

The Doctor smiled wistfully. "Won't the first time I've committed genocide."

Jack met his old Time Lord friend's gaze. "Thank you."

* * *

**Just a little explanation for the Doctor's names in his small monologue up there.**

**"Oncoming Storm" - called by the Daleks**

**"Karshtakavaar" - Draconian for Oncoming Storm**

******"Ka Faraq Gatri" - called by the Daleks, means bringer of darkness/destroyer of worlds**

******"The Lonely Angel" - called by Reniette**

******"Time's Champion" - title bestowed on the Seventh Doctor for his service to time**


	11. Pandorica Countdown

The rest of the Torchwood team was busy aiding survivors, leaving Amy, Jack and the Doctor alone in the Hub. "Not bad, Torchwood," the Doctor smiled. "Better now though. Hopefully, will be." The Doctor threw Jack a piece of twine. On the end of it was a key. "It's yours if you want it." It was the Doctor's way of inviting Jack back on board the TARDIS.

Jack fingered the twine and gazed at the key longingly. He wanted to get away, to leave the world behind. But he also had a duty. "Maybe some other time." He threw the key back which was promptly flung back to him.

"Keep it anyway. And come inside the TARDIS again if nothing else."

"If she'll let me back in."

"She loves a visitor every once in a while. Likes to flaunt her new interior." The Doctor snapped his fingers. The police box door creaked open a bit. "You can do that now?" inquired Jack with awe.

"Like it. A little flashy don't you think?"

"Showing off."

"What he does best," sighed Amy.

"Ego size of the Medusa Cascade," agreed Jack.

"Oi!" the Doctor protested. The two companions shared a laugh. "Well there she is." The Doctor gestured for Jack to enter. "All new, sexy and magnificent."

Jack pushed open the door, his eyes wide. Stepping inside he commented, "Well… It's bigger than bigger on the inside. I feel like I've fallen down the rabbit hole. Why is she all different?" Jack began to circle the console, patting it and touching it like he used to do.

"I didn't want to go," the Time Lord said with far off eyes, "so I regenerated rather violently."

Jack looked up with his hand still on the console. "Seems a bit cluttered though." At that moment the part of the console Jack was touching sparked. The immortal yelped and removed his hand to inspect the burn that promptly disappeared.

"Careful. She's still as picky as ever."

"Sorry girl," Jack whispered. "Did you miss me?" The lights inside the time ship dimmed in a sort of response. The three travelers looked up and saw the ceiling lights flickered.

"Well that's odd," the Doctor remarked, immediately leaning to the console. He inspected the new screen for scans and fiddled with the knobs. "No, no, no! Now isn't the time to have a mind of your own girl!"

The end of the TARDIS console facing the entrance sparked open and a bright light shot out –the Heart of the TARDIS. "Not now!" the Doctor exclaimed again.

"Doctor!" Amy cried.

"Doctor," Jack warned.

"I'm not doing anything!" the Doctor shouted back. He desperately tried to stop what was going on but the light was too bright. None of them could do anything but shield their eyes. Then, as suddenly as the Heart popped out of the console, it swished back in.

"What happened?" Amy asked, propping herself from off the floor, helping the Doctor do the same. Jack pushed himself against the railing to regain his balance.

"Dunno," whispered the Time Lord.

_Well that was certainly interesting._

Jack spun around, his coat twirling. "What was that?" he asked.

"What was what?" the Doctor responded.

"That, that voice!"

"What voice?"

_Stop spinning around sir. It's making your coat look like a terrible imitation of a ballet dancer._

"There it is again!" Jack cried. "It sounds… it sounds like…"

_Could your Sherlock Holmes deduction skills be any duller?_

"What are you talking about?" the Doctor frowned, walking up to the captain. He pressed his hands on both side of Jack's head. "Wow."

"What?"

The Doctor dropped his hands. "_Who_ does it sound like?"

Jack paused. "I said I wouldn't-"

"Yeah yeah yeah. You promised not to say his name again. Who was it Captain?"

"… Ianto."

"Exactly! Bloody TARDIS. Sometimes it's good for her to have a mind of her own. You clever girl." The Doctor tapped the console. "Lovely!"

"But-"

"Ianto Jones! Formerly Torchwood Three, but before that he was with Torchwood One. Bloody Hartman, but besides that, London wanted all the best employees. They had to have a certain degree of natural psychic ability. Then they'd train the workers further. That's why the paper didn't work. But so! You Jack, 51st century. Natural abilities have developed by then. The two of you form this kind of a bond. Let me guess. Ianto was always a bit upset when you died."

"Yeah, I-"

"That's the bond. It's like your personality is in his and vice versa, only they're both dormant. Now the TARDIS, she got all inside your head, and awoke the dormant part."

"So it's like Ianto, he can talk to Jack," Amy realized.

"Synaptic imprint. It's a bit more complicated than that. Captain?" Jack had been staring at the Doctor blankly for the entire duration of the explanation. "Captain?"

"Sorry. This is a lot of information to digest," Jack laughed uneasily.

"You'll get used to it."

_You never let anything else stop you before_, the voice in Jack's head –Ianto- teased.

"Wow…" mouthed Jack.

_It also means that I knew you loved me._

"I, uh…" Jack was still at a loss for words.

"Isn't this just great though? More than 900 years of time travel and she's still full of surprises." The Doctor beamed. "Clever, clever, clever."

_Say something Jack. They're going to start to believe you've gone mute._

"I promised I wouldn't forget him," Jack told the Doctor.

_Was that the best you could come up with, _sir_? Not the classiest line during a life-changing milestone in your life._

The Doctor's voice softened. "Now you never will."

_I asked for one thousand years and this is what I get. I should have asked for more._

_And I would have given it_, Jack smiled softly at Ianto's sarcasm. It was a gentle grin that hadn't graced his lips in a thousand years. "Well then Doctor," Jack said, finally regaining his charisma. He headed for the TARDIS's door. "Should be going. World to save and protect."

_You work too hard,_ Ianto scolded.

"Responsibility. Can't argue with that."

Jack chuckled. "I've heard that before. And could you…" Jack gestured to his Vortex manipulator.

The Doctor rolled his eyes and twirled out his sonic screwdriver. "Teleports _only_ though," the Doctor said. "Don't try anything fishy." He turned to Amy. "Fish custard, get it?" Amy smiled back.

Jack straightened up and saluted. The Doctor nodded back. "The Time Lord I knew once would wince at that," commented the immortal.

"I've changed too."

"No doubt," Jack smirked. "I'll be seeing you then." With that, he left the time ship.

"Will he be alright?" Amy asked. The Doctor didn't respond for a moment. "Doctor?"

"Naw. Not alright. He'll be a bit better though. There's a lot he still has to do, horrors to face."

"Will we see him again?"

"Maybe. Who knows? But for now, how does Barcelona sound?"

"Spain?" Amy drawled in her Scottish accent. "You said no where boring!"

"Not Spain you silly. Barcelona the planet!"

"There's a _planet_ called Barcelona?"

"Dogs with no noses."

"Is that even possible?"

"Obviously."

Then it dawned on Amy. "But Doctor, the Daleks, those 'Cybermen' and those planets in the sky. I don't remember any of that. Why do I remember the 456?"

* * *

**Supposed to be one of those allusions to the finale...**

**CAN'T WAIT FOR SATURDAY**

**Be sure to read the Coda and deleted scene.**


	12. Coda

Jack Harkness outlives his team. Nothing unexpected there. He's immortal after all.

* * *

Emily grows up to be a part of the new team. She feels like she shouldn't trust this man, but she can't remember for what reason.

* * *

Two pairs of eyes meet. One pair green, the other hazel. There's a soft engine hum in the background. "I don't know."

* * *

Jack starts to realize that the Nyalaxo incident has been forgotten. It's not the perception filther though. He'd gotten rid of that ages ago. It's something else. Why isn't it affecting him? He sends a message to the Doctor, but knowing him it'll be a while.

* * *

The two pairs of eyes waver for a moment. "I don't know," he repeats.


	13. OUTTAKE DELETED SCENE

**I was going to have a scene where the Doctor further explains his connection to Jack. This was where he talked about the events in Children of Earth and Jack's immortality. This was to be inserted after Jack discovers the Doctor and the Doctor is rewiring stuff. I ended up coming up with a more suitable plot line so I scratched this out. It was also a bit wordy and too much explanation.**

**Small _The Beast Below_ ref at the end that I liked. Also a small ref to the Doctor's unvoiced romance with Rose. Sorry Amy/Doctor shippers. I don't like it that much. Rory's cuter.**

**

* * *

**

"Are you going to explain now?" Amy asked, tapping her foot.

"Saving the world, not a lot of time. Very complicated. Maybe later."

"So multitask, c'mon."

"I knew him before. He was as companion, a traveler. 51st century, like River Song, no association though. Part of the Time Agency. It's like the time police. Some stuff happened and he left them hiding out in the London Blitz. Found him while I was traveling with this other girl, Rose. He tagged alone and then we came to the Daleks."

"Like Churchill's Daleks?"

"Yes but not quite. These were the real Daleks. The Ironsides were impure, but that's not the point. The point is that Jack died."

"Yeah, but he's here right now."

"Yes, and I also mentioned that he was immortal. I sent Rose back to Earth, back to safety and she came back. Absorbed the Heart of the TARDIS to try and save us. Destroyed all the Daleks and brought Jack back forever. She couldn't control that power."

"Hold up. What do you mean the Heart of the TARDIS?"

"She's alive."

"No way really?"

"Where were you when I said that before? Did you think that a TARDIS was _built_?"

"Yes, I-"

"Moving on."

"Then what about the gun Doctor? He looked like he was going to kill you. What was that all about? The Silo? Utopia?"

"A long story. You don't remember it."

"Just because I don't remember anything about the Daleks doesn't mean that I don't remember anything at all."

"No I mean you really don't remember it. It was the Year that Never Was. A paradox that no remembers except for those in the eye of the storm."

"Summary then?"

The Doctor's shoulders drooped as he thought about the Master. "Harold Saxon, the PM? Remember him? I knew him as the Master. He was a Time Lord. He wanted a new Gallifrey. He'd been hiding at the end of the universe, memories erased. It was a crazy time. Refugees were hiding out in what they called the Silo. They all believed in a brand new world called Utopia.

"It didn't work out. The Master regained his memories and stole the TARDIS. When we came back, Jack, Martha and I, we missed the elections. We were public enemies of the state by Harold Saxon."

"Hang on," Amy cut in. "I've seen Jack before. On the telly! And the other girl. But that wasn't you. The other picture. You look totally different."

"Regeneration. It's a Time Lord trick. When we first met, remember that? Back when you were a little girl. I fell out of the TARDIS clutching my chest and breathed out this golden air, telling you I was still cooking? Anyway, we tried to save the world. Some things happened along the way and Saxon tortured Jack for a whole virtual year. He wasn't the same after that but he put on a good show of being brave. I fixed things up and here we are."

"Yeah, but why did he want _kill_ you?" Amy reiterated.

"The Nyaloxo"

"What's that? You said 456. Do you mean-"

"September 2009. Yes. Children talking. The Nyalaxo are addicted to the hormones prepubescent kids produce. Like a drug. And Jack saved the world. Brave old Jack. Him and his old Torchwood team. But…"

"He lost," finished Amy.

"Everything. His lover was killed. He sacrificed his grandson and his daughter disowned him."

"Grandson?" Amy repeated. "How could, I mean, why would-"

"The star whale Amy," the Doctor said, stripping a wire and twisting it to another one. "One creature or hundreds more. One child or the children of Earth." The Doctor pocketed his sonic screwdriver and faced Amy. "He couldn't stand and watch the children cry." Amy looked back into those eyes are saw something between regret and sorrow. "He's a fixed point in time and space, a fact. Never-changing, always constant. While everything around him dies, he'll still be around. He's going to outlive even me. That kind of loss and hurt is enough to drive anyone mad."

"That's why he wanted to kill then. But he's still here," Amy said. "That's got to mean something. And you said he was like you."

"I lose everyone too, just not to death. One day, you're going to grow up even more. You'll want to start a life of your own and I have to learn to let go."

"I want to explore the universe forever."

"That's what Rose said," the Doctor replied sadly. "Years ago. Rose, sweet Rose. Lovely, lovely Rose. She's happier now."

"Did you love her?"

The Doctor merely smiled as he checked the systems so Amy decided to change the subject slightly. "Very old, very kind and very, very last of its kind?"

The Doctor looked up. "Yeah. Something like that."


End file.
